SNP pipeline analysis of subjects with 3 body site results

library(tidyverse)
source("MAP_functions.R")

Subject 26

SNP_analysis_pipeline(subject_id = 26)

[1] "SUBJECT_ID is 26"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  29845"
[1] "Num bases in R recomb = blocks 29845"
[1] "Num bases in V recomb = blocks 8898"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036306"
[1] "Numbers of C bases above cutoff is  1036204"
[1] "Numbers of V bases above cutoff is  1035660"
[1] "Number of iSNP positions =  5311"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  36"
[1] "R only rare iSNPs (RonlyRIrare) =  16"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  4"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  6"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5229"
[1] "All rare fixed SNPs (AllFrare) =  1179"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  22"
[1] "All iSNPs (AllRI) =  16"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  1"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 28 rows containing missing values (geom_point).
Warning: Removed 35 rows containing missing values (geom_point).
Warning: Removed 27 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1049"
[1] "Number cDenovo Non-Ref SNPs for C =  4421"
[1] "Number cDenovo iSNPs for C =  1"
[1] "Number cDenovo Ref SNPs for R =  1050"
[1] "Number cDenovo Non-Ref SNPs for R =  4413"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  1052"
[1] "Number cDenovo Non-Ref SNPs for V =  4419"
[1] "Number cDenovo iSNPs for V =  1"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 90 rows containing non-finite values (stat_boxplot).

Subject 32

SNP_analysis_pipeline(subject_id = 32)

[1] "SUBJECT_ID is 32"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  8083"
[1] "Num bases in R recomb = blocks 7903"
[1] "Num bases in V recomb = blocks 66553"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1035511"
[1] "Numbers of C bases above cutoff is  939599"
[1] "Numbers of V bases above cutoff is  1036507"
[1] "Number of iSNP positions =  5168"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  13"
[1] "R only rare iSNPs (RonlyRIrare) =  1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  13"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  23"
[1] "C only rare iSNPs (ConlyRIrare) =  20"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  576"
[1] "V only rare iSNPs (VonlyRIrare) =  266"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  137"
[1] "RC only fixed SNPs (RConlyF) =  13"
[1] "RC only rare fixed SNPs (RConlyFrare) =  13"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  726"
[1] "All rare fixed SNPs (AllFrare) =  508"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  294"
[1] "All iSNPs (AllRI) =  11"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  1"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  1"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  416"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  1"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 596 rows containing missing values (geom_point).
Warning: Removed 38 rows containing missing values (geom_point).
Warning: Removed 32 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1062"
[1] "Number cDenovo Non-Ref SNPs for C =  3824"
[1] "Number cDenovo iSNPs for C =  21"
[1] "Number cDenovo Ref SNPs for R =  1137"
[1] "Number cDenovo Non-Ref SNPs for R =  4328"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  685"
[1] "Number cDenovo Non-Ref SNPs for V =  614"
[1] "Number cDenovo iSNPs for V =  4172"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 666 rows containing non-finite values (stat_boxplot).

Subject 68

SNP_analysis_pipeline(subject_id = 68)

[1] "SUBJECT_ID is 68"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  66"
[1] "Num bases in R recomb = blocks 206"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1033503"
[1] "Numbers of C bases above cutoff is  1035903"
[1] "Numbers of V bases above cutoff is  1034542"
[1] "Number of iSNP positions =  5247"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  6"
[1] "R only rare iSNPs (RonlyRIrare) =  1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  4"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  2"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5189"
[1] "All rare fixed SNPs (AllFrare) =  1006"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  11"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  6"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 28 rows containing missing values (geom_point).
Warning: Removed 43 rows containing missing values (geom_point).
Warning: Removed 22 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1062"
[1] "Number cDenovo Non-Ref SNPs for C =  4408"
[1] "Number cDenovo iSNPs for C =  1"
[1] "Number cDenovo Ref SNPs for R =  1059"
[1] "Number cDenovo Non-Ref SNPs for R =  4397"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  1069"
[1] "Number cDenovo Non-Ref SNPs for V =  4404"
[1] "Number cDenovo iSNPs for V =  4"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 93 rows containing non-finite values (stat_boxplot).

Subject 72

SNP_analysis_pipeline(subject_id = 72)

[1] "SUBJECT_ID is 72"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  73166"
[1] "Num bases in R recomb = blocks 73117"
[1] "Num bases in V recomb = blocks 65240"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  344563"
[1] "Numbers of C bases above cutoff is  1011352"
[1] "Numbers of V bases above cutoff is  1029389"
[1] "Number of iSNP positions =  617"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  49"
[1] "R only rare iSNPs (RonlyRIrare) =  44"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  35"
[1] "V only rare iSNPs (VonlyRIrare) =  22"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  9"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  1"
[1] "All fixed SNPs (AllF) =  512"
[1] "All rare fixed SNPs (AllFrare) =  295"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  97"
[1] "All iSNPs (AllRI) =  1"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 208 rows containing missing values (geom_point).
Warning: Removed 3480 rows containing missing values (geom_point).
Warning: Removed 97 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4253"
[1] "Number cDenovo Non-Ref SNPs for C =  1042"
[1] "Number cDenovo iSNPs for C =  5"
[1] "Number cDenovo Ref SNPs for R =  1638"
[1] "Number cDenovo Non-Ref SNPs for R =  390"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  4346"
[1] "Number cDenovo Non-Ref SNPs for V =  1065"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 3785 rows containing non-finite values (stat_boxplot).

Subject 87

SNP_analysis_pipeline(subject_id = 87)

[1] "SUBJECT_ID is 87"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1016254"
[1] "Numbers of C bases above cutoff is  1035662"
[1] "Numbers of V bases above cutoff is  1025249"
[1] "Number of iSNP positions =  1200"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  77"
[1] "R only rare iSNPs (RonlyRIrare) =  55"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  3"
[1] "C only rare iSNPs (ConlyRIrare) =  3"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  61"
[1] "V only rare iSNPs (VonlyRIrare) =  40"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  3"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  992"
[1] "All rare fixed SNPs (AllFrare) =  690"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  1"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  1"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  4"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  5"

Warning: Removed 27 rows containing missing values (geom_point).
Warning: Removed 156 rows containing missing values (geom_point).
Warning: Removed 87 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4594"
[1] "Number cDenovo Non-Ref SNPs for C =  863"
[1] "Number cDenovo iSNPs for C =  6"
[1] "Number cDenovo Ref SNPs for R =  4476"
[1] "Number cDenovo Non-Ref SNPs for R =  815"
[1] "Number cDenovo iSNPs for R =  43"
[1] "Number cDenovo Ref SNPs for V =  4527"
[1] "Number cDenovo Non-Ref SNPs for V =  835"
[1] "Number cDenovo iSNPs for V =  41"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 270 rows containing non-finite values (stat_boxplot).

Subject 98

SNP_analysis_pipeline(subject_id = 98)

[1] "SUBJECT_ID is 98"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  245"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1038078"
[1] "Numbers of C bases above cutoff is  1004338"
[1] "Numbers of V bases above cutoff is  1035500"
[1] "Number of iSNP positions =  1301"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  27"
[1] "R only rare iSNPs (RonlyRIrare) =  15"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  47"
[1] "V only rare iSNPs (VonlyRIrare) =  39"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  31"
[1] "RV only rare iSNPs (RVonlyRIrare) =  3"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  1159"
[1] "All rare fixed SNPs (AllFrare) =  792"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  3"
[1] "All iSNPs (AllRI) =  3"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  13"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 230 rows containing missing values (geom_point).
Warning: Removed 33 rows containing missing values (geom_point).
Warning: Removed 48 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4459"
[1] "Number cDenovo Non-Ref SNPs for C =  817"
[1] "Number cDenovo iSNPs for C =  6"
[1] "Number cDenovo Ref SNPs for R =  4613"
[1] "Number cDenovo Non-Ref SNPs for R =  866"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  4606"
[1] "Number cDenovo Non-Ref SNPs for V =  858"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 311 rows containing non-finite values (stat_boxplot).

Subject 107

SNP_analysis_pipeline(subject_id = 107)

[1] "SUBJECT_ID is 107"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036634"
[1] "Numbers of C bases above cutoff is  792534"
[1] "Numbers of V bases above cutoff is  1029789"
[1] "Number of iSNP positions =  3726"
[1] "R only fixed SNPs (RonlyF) =  2"
[1] "R only rare fixed SNPs (RonlyFrare) =  2"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  34"
[1] "R only rare iSNPs (RonlyRIrare) =  13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  34"
[1] "C only rare iSNPs (ConlyRIrare) =  34"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  65"
[1] "V only rare iSNPs (VonlyRIrare) =  51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  25"
[1] "RV only rare iSNPs (RVonlyRIrare) =  4"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  3546"
[1] "All rare fixed SNPs (AllFrare) =  674"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  0"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 1496 rows containing missing values (geom_point).
Warning: Removed 32 rows containing missing values (geom_point).
Warning: Removed 62 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  819"
[1] "Number cDenovo Non-Ref SNPs for C =  3182"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1064"
[1] "Number cDenovo Non-Ref SNPs for R =  4401"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  1057"
[1] "Number cDenovo Non-Ref SNPs for V =  4378"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 1590 rows containing non-finite values (stat_boxplot).

Subject 192

SNP_analysis_pipeline(subject_id = 192)

[1] "SUBJECT_ID is 192"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  50904"
[1] "Num bases in R recomb = blocks 50443"
[1] "Num bases in V recomb = blocks 50443"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036095"
[1] "Numbers of C bases above cutoff is  1028769"
[1] "Numbers of V bases above cutoff is  1037030"
[1] "Number of iSNP positions =  5297"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  20"
[1] "R only rare iSNPs (RonlyRIrare) =  13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  1"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  64"
[1] "V only rare iSNPs (VonlyRIrare) =  51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  3"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  2"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  46"
[1] "RV only rare iSNPs (RVonlyRIrare) =  7"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5115"
[1] "All rare fixed SNPs (AllFrare) =  1215"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  63"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  2"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  4"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 78 rows containing missing values (geom_point).
Warning: Removed 27 rows containing missing values (geom_point).
Warning: Removed 21 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1233"
[1] "Number cDenovo Non-Ref SNPs for C =  4193"
[1] "Number cDenovo iSNPs for C =  3"
[1] "Number cDenovo Ref SNPs for R =  1252"
[1] "Number cDenovo Non-Ref SNPs for R =  4227"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  1249"
[1] "Number cDenovo Non-Ref SNPs for V =  4236"
[1] "Number cDenovo iSNPs for V =  1"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 126 rows containing non-finite values (stat_boxplot).

Subject 227

SNP_analysis_pipeline(subject_id = 227)

[1] "SUBJECT_ID is 227"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  954"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 945"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  822591"
[1] "Numbers of C bases above cutoff is  1034715"
[1] "Numbers of V bases above cutoff is  1038235"
[1] "Number of iSNP positions =  999"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  178"
[1] "R only rare iSNPs (RonlyRIrare) =  149"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  3"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  798"
[1] "All rare fixed SNPs (AllFrare) =  540"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  15"
[1] "All iSNPs (AllRI) =  4"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 35 rows containing missing values (geom_point).
Warning: Removed 1171 rows containing missing values (geom_point).
Warning: Removed 24 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4631"
[1] "Number cDenovo Non-Ref SNPs for C =  825"
[1] "Number cDenovo iSNPs for C =  7"
[1] "Number cDenovo Ref SNPs for R =  3677"
[1] "Number cDenovo Non-Ref SNPs for R =  623"
[1] "Number cDenovo iSNPs for R =  27"
[1] "Number cDenovo Ref SNPs for V =  4645"
[1] "Number cDenovo Non-Ref SNPs for V =  826"
[1] "Number cDenovo iSNPs for V =  3"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 1230 rows containing non-finite values (stat_boxplot).

Subject 362

SNP_analysis_pipeline(subject_id = 362)

[1] "SUBJECT_ID is 362"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 160315"
[1] "Num bases in V recomb = blocks 160315"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1031572"
[1] "Numbers of C bases above cutoff is  1032552"
[1] "Numbers of V bases above cutoff is  1038383"
[1] "Number of iSNP positions =  2002"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  10"
[1] "R only rare iSNPs (RonlyRIrare) =  9"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  1"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  4"
[1] "C only rare iSNPs (ConlyRIrare) =  4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  3"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  5"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  1944"
[1] "All rare fixed SNPs (AllFrare) =  879"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  790"
[1] "All iSNPs (AllRI) =  13"
[1] "All rare  iSNPs (AllRIrare) =  1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  2"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  2"

Warning: Removed 49 rows containing missing values (geom_point).
Warning: Removed 60 rows containing missing values (geom_point).
Warning: Removed 15 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  3987"
[1] "Number cDenovo Non-Ref SNPs for C =  1451"
[1] "Number cDenovo iSNPs for C =  6"
[1] "Number cDenovo Ref SNPs for R =  3973"
[1] "Number cDenovo Non-Ref SNPs for R =  1454"
[1] "Number cDenovo iSNPs for R =  6"
[1] "Number cDenovo Ref SNPs for V =  4008"
[1] "Number cDenovo Non-Ref SNPs for V =  1457"
[1] "Number cDenovo iSNPs for V =  13"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 124 rows containing non-finite values (stat_boxplot).

Subject 519

SNP_analysis_pipeline(subject_id = 519)

[1] "SUBJECT_ID is 519"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  431"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 226"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  818552"
[1] "Numbers of C bases above cutoff is  1020321"
[1] "Numbers of V bases above cutoff is  1034717"
[1] "Number of iSNP positions =  3957"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  27"
[1] "R only rare iSNPs (RonlyRIrare) =  27"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  3"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  3913"
[1] "All rare fixed SNPs (AllFrare) =  780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  17"
[1] "All iSNPs (AllRI) =  4"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 150 rows containing missing values (geom_point).
Warning: Removed 1181 rows containing missing values (geom_point).
Warning: Removed 32 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1052"
[1] "Number cDenovo Non-Ref SNPs for C =  4295"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  910"
[1] "Number cDenovo Non-Ref SNPs for R =  3402"
[1] "Number cDenovo iSNPs for R =  4"
[1] "Number cDenovo Ref SNPs for V =  1069"
[1] "Number cDenovo Non-Ref SNPs for V =  4396"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 1363 rows containing non-finite values (stat_boxplot).

Subject 564

SNP_analysis_pipeline(subject_id = 564)

[1] "SUBJECT_ID is 564"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 24734"
[1] "Num bases in V recomb = blocks 24734"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1035161"
[1] "Numbers of C bases above cutoff is  1030082"
[1] "Numbers of V bases above cutoff is  1013781"
[1] "Number of iSNP positions =  5253"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  0"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  231"
[1] "C only rare fixed SNPs (ConlyFrare) =  57"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  126"
[1] "C only iSNPs (ConlyRI) =  4"
[1] "C only rare iSNPs (ConlyRIrare) =  4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  58"
[1] "V only rare iSNPs (VonlyRIrare) =  53"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  179"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  96"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  78"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  4668"
[1] "All rare fixed SNPs (AllFrare) =  881"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  32"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  1"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 75 rows containing missing values (geom_point).
Warning: Removed 29 rows containing missing values (geom_point).
Warning: Removed 189 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1061"
[1] "Number cDenovo Non-Ref SNPs for C =  4365"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1062"
[1] "Number cDenovo Non-Ref SNPs for R =  4406"
[1] "Number cDenovo iSNPs for R =  4"
[1] "Number cDenovo Ref SNPs for V =  1029"
[1] "Number cDenovo Non-Ref SNPs for V =  4224"
[1] "Number cDenovo iSNPs for V =  59"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 293 rows containing non-finite values (stat_boxplot).

Subject 753

SNP_analysis_pipeline(subject_id = 753)

[1] "SUBJECT_ID is 753"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  619998"
[1] "Numbers of C bases above cutoff is  1037605"
[1] "Numbers of V bases above cutoff is  1037470"
[1] "Number of iSNP positions =  912"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  233"
[1] "R only rare iSNPs (RonlyRIrare) =  105"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  623"
[1] "All rare fixed SNPs (AllFrare) =  426"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  2"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  9"

Warning: Removed 17 rows containing missing values (geom_point).
Warning: Removed 2100 rows containing missing values (geom_point).
Warning: Removed 23 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4617"
[1] "Number cDenovo Non-Ref SNPs for C =  851"
[1] "Number cDenovo iSNPs for C =  5"
[1] "Number cDenovo Ref SNPs for R =  2768"
[1] "Number cDenovo Non-Ref SNPs for R =  483"
[1] "Number cDenovo iSNPs for R =  139"
[1] "Number cDenovo Ref SNPs for V =  4610"
[1] "Number cDenovo Non-Ref SNPs for V =  853"
[1] "Number cDenovo iSNPs for V =  4"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 2140 rows containing non-finite values (stat_boxplot).

Subject 908

SNP_analysis_pipeline(subject_id = 908)

[1] "SUBJECT_ID is 908"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 700"
[1] "Num bases in V recomb = blocks 494"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1033470"
[1] "Numbers of C bases above cutoff is  1032274"
[1] "Numbers of V bases above cutoff is  1006412"
[1] "Number of iSNP positions =  5112"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  0"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  15"
[1] "C only rare iSNPs (ConlyRIrare) =  6"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  86"
[1] "V only rare iSNPs (VonlyRIrare) =  80"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  4852"
[1] "All rare fixed SNPs (AllFrare) =  928"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  8"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  5"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 39 rows containing missing values (geom_point).
Warning: Removed 42 rows containing missing values (geom_point).
Warning: Removed 195 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1059"
[1] "Number cDenovo Non-Ref SNPs for C =  4392"
[1] "Number cDenovo iSNPs for C =  6"
[1] "Number cDenovo Ref SNPs for R =  1063"
[1] "Number cDenovo Non-Ref SNPs for R =  4391"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  1031"
[1] "Number cDenovo Non-Ref SNPs for V =  4174"
[1] "Number cDenovo iSNPs for V =  96"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 276 rows containing non-finite values (stat_boxplot).

Subject 927

SNP_analysis_pipeline(subject_id = 927)

[1] "SUBJECT_ID is 927"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  37976"
[1] "Num bases in R recomb = blocks 37162"
[1] "Num bases in V recomb = blocks 37632"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1026496"
[1] "Numbers of C bases above cutoff is  1034845"
[1] "Numbers of V bases above cutoff is  1034464"
[1] "Number of iSNP positions =  5283"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  2"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  4"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5244"
[1] "All rare fixed SNPs (AllFrare) =  1247"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  183"
[1] "All iSNPs (AllRI) =  24"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  5"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 34 rows containing missing values (geom_point).
Warning: Removed 91 rows containing missing values (geom_point).
Warning: Removed 53 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1075"
[1] "Number cDenovo Non-Ref SNPs for C =  4378"
[1] "Number cDenovo iSNPs for C =  2"
[1] "Number cDenovo Ref SNPs for R =  1057"
[1] "Number cDenovo Non-Ref SNPs for R =  4337"
[1] "Number cDenovo iSNPs for R =  4"
[1] "Number cDenovo Ref SNPs for V =  1071"
[1] "Number cDenovo Non-Ref SNPs for V =  4362"
[1] "Number cDenovo iSNPs for V =  3"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 178 rows containing non-finite values (stat_boxplot).

Subject 951

SNP_analysis_pipeline(subject_id = 951)

[1] "SUBJECT_ID is 951"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  14329"
[1] "Num bases in R recomb = blocks 16927"
[1] "Num bases in V recomb = blocks 14329"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1013234"
[1] "Numbers of C bases above cutoff is  1035195"
[1] "Numbers of V bases above cutoff is  1035300"
[1] "Number of iSNP positions =  5191"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  14"
[1] "R only rare iSNPs (RonlyRIrare) =  2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  8"
[1] "V only rare iSNPs (VonlyRIrare) =  1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  2"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5069"
[1] "All rare fixed SNPs (AllFrare) =  1083"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  106"
[1] "All iSNPs (AllRI) =  17"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  4"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  18"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 25 rows containing missing values (geom_point).
Warning: Removed 198 rows containing missing values (geom_point).
Warning: Removed 29 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1137"
[1] "Number cDenovo Non-Ref SNPs for C =  4339"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1100"
[1] "Number cDenovo Non-Ref SNPs for R =  4202"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  1134"
[1] "Number cDenovo Non-Ref SNPs for V =  4336"
[1] "Number cDenovo iSNPs for V =  2"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 252 rows containing non-finite values (stat_boxplot).

Subject 968

SNP_analysis_pipeline(subject_id = 968)

[1] "SUBJECT_ID is 968"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  578500"
[1] "Numbers of C bases above cutoff is  1029349"
[1] "Numbers of V bases above cutoff is  1037840"
[1] "Number of iSNP positions =  1245"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  537"
[1] "R only rare iSNPs (RonlyRIrare) =  114"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  586"
[1] "All rare fixed SNPs (AllFrare) =  403"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  9"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  19"

Warning: Removed 71 rows containing missing values (geom_point).
Warning: Removed 2300 rows containing missing values (geom_point).
Warning: Removed 19 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4595"
[1] "Number cDenovo Non-Ref SNPs for C =  823"
[1] "Number cDenovo iSNPs for C =  6"
[1] "Number cDenovo Ref SNPs for R =  2304"
[1] "Number cDenovo Non-Ref SNPs for R =  438"
[1] "Number cDenovo iSNPs for R =  453"
[1] "Number cDenovo Ref SNPs for V =  4643"
[1] "Number cDenovo Non-Ref SNPs for V =  828"
[1] "Number cDenovo iSNPs for V =  5"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 2390 rows containing non-finite values (stat_boxplot).

Subject 1077

SNP_analysis_pipeline(subject_id = 1077)

[1] "SUBJECT_ID is 1077"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  10689"
[1] "Num bases in R recomb = blocks 9806"
[1] "Num bases in V recomb = blocks 10291"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  798730"
[1] "Numbers of C bases above cutoff is  1036188"
[1] "Numbers of V bases above cutoff is  979111"
[1] "Number of iSNP positions =  3956"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  154"
[1] "R only rare iSNPs (RonlyRIrare) =  109"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  14"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  59"
[1] "V only rare iSNPs (VonlyRIrare) =  47"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  1"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  3145"
[1] "All rare fixed SNPs (AllFrare) =  620"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  104"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  2"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  26"

Warning: Removed 30 rows containing missing values (geom_point).
Warning: Removed 1387 rows containing missing values (geom_point).
Warning: Removed 366 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1064"
[1] "Number cDenovo Non-Ref SNPs for C =  4405"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  771"
[1] "Number cDenovo Non-Ref SNPs for R =  2914"
[1] "Number cDenovo iSNPs for R =  427"
[1] "Number cDenovo Ref SNPs for V =  985"
[1] "Number cDenovo Non-Ref SNPs for V =  4121"
[1] "Number cDenovo iSNPs for V =  27"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 1783 rows containing non-finite values (stat_boxplot).

Subject 1078

SNP_analysis_pipeline(subject_id = 1078)

[1] "SUBJECT_ID is 1078"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 26229"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  875018"
[1] "Numbers of C bases above cutoff is  249618"
[1] "Numbers of V bases above cutoff is  1015869"
[1] "Number of iSNP positions =  1382"
[1] "R only fixed SNPs (RonlyF) =  96"
[1] "R only rare fixed SNPs (RonlyFrare) =  40"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  4"
[1] "R only iSNPs (RonlyRI) =  103"
[1] "R only rare iSNPs (RonlyRIrare) =  65"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  12"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  85"
[1] "C only rare iSNPs (ConlyRIrare) =  74"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  4"
[1] "V only fixed SNPs (VonlyF) =  1"
[1] "V only rare fixed SNPs (VonlyFrare) =  1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  35"
[1] "V only rare iSNPs (VonlyRIrare) =  34"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  1"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  33"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  91"
[1] "RV only rare iSNPs (RVonlyRIrare) =  5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  9"
[1] "VC only fixed SNPs (VConlyF) =  4"
[1] "VC only rare fixed SNPs (VConlyFrare) =  2"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  17"
[1] "VC only rare iSNPs (VConlyRIrare) =  10"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  1"
[1] "All fixed SNPs (AllF) =  32"
[1] "All rare fixed SNPs (AllFrare) =  32"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  65"
[1] "All rare  iSNPs (AllRIrare) =  1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  51"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  54"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  58"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  8"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  5"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  58"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  58"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 4187 rows containing missing values (geom_point).
Warning: Removed 915 rows containing missing values (geom_point).
Warning: Removed 67 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  599"
[1] "Number cDenovo Non-Ref SNPs for C =  54"
[1] "Number cDenovo iSNPs for C =  617"
[1] "Number cDenovo Ref SNPs for R =  874"
[1] "Number cDenovo Non-Ref SNPs for R =  3074"
[1] "Number cDenovo iSNPs for R =  594"
[1] "Number cDenovo Ref SNPs for V =  2010"
[1] "Number cDenovo Non-Ref SNPs for V =  249"
[1] "Number cDenovo iSNPs for V =  3131"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 5169 rows containing non-finite values (stat_boxplot).

Subject 1079

SNP_analysis_pipeline(subject_id = 1079)

[1] "SUBJECT_ID is 1079"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  24626"
[1] "Num bases in R recomb = blocks 25420"
[1] "Num bases in V recomb = blocks 24894"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1018215"
[1] "Numbers of C bases above cutoff is  1036824"
[1] "Numbers of V bases above cutoff is  1035527"
[1] "Number of iSNP positions =  5450"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  299"
[1] "R only rare iSNPs (RonlyRIrare) =  137"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  3"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  22"
[1] "V only rare iSNPs (VonlyRIrare) =  8"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  2"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  19"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  2169"
[1] "All rare fixed SNPs (AllFrare) =  858"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  104"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  10"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  13"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  132"

Warning: Removed 24 rows containing missing values (geom_point).
Warning: Removed 155 rows containing missing values (geom_point).
Warning: Removed 28 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1056"
[1] "Number cDenovo Non-Ref SNPs for C =  4412"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  764"
[1] "Number cDenovo Non-Ref SNPs for R =  1978"
[1] "Number cDenovo iSNPs for R =  2595"
[1] "Number cDenovo Ref SNPs for V =  1018"
[1] "Number cDenovo Non-Ref SNPs for V =  4034"
[1] "Number cDenovo iSNPs for V =  412"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 207 rows containing non-finite values (stat_boxplot).

Subject 1106

SNP_analysis_pipeline(subject_id = 1106)

[1] "SUBJECT_ID is 1106"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  21790"
[1] "Num bases in R recomb = blocks 21569"
[1] "Num bases in V recomb = blocks 3423"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1024517"
[1] "Numbers of C bases above cutoff is  1032626"
[1] "Numbers of V bases above cutoff is  1038242"
[1] "Number of iSNP positions =  692"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  0"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  1"
[1] "V only rare iSNPs (VonlyRIrare) =  1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  1"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  667"
[1] "All rare fixed SNPs (AllFrare) =  425"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  138"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  1"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  7"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 63 rows containing missing values (geom_point).
Warning: Removed 116 rows containing missing values (geom_point).
Warning: Removed 26 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4949"
[1] "Number cDenovo Non-Ref SNPs for C =  502"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  4902"
[1] "Number cDenovo Non-Ref SNPs for R =  496"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  4986"
[1] "Number cDenovo Non-Ref SNPs for V =  502"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 205 rows containing non-finite values (stat_boxplot).

Subject 1145

SNP_analysis_pipeline(subject_id = 1145)

[1] "SUBJECT_ID is 1145"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  474"
[1] "Num bases in R recomb = blocks 261"
[1] "Num bases in V recomb = blocks 177"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1026277"
[1] "Numbers of C bases above cutoff is  1034922"
[1] "Numbers of V bases above cutoff is  888302"
[1] "Number of iSNP positions =  4468"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  3"
[1] "R only rare iSNPs (RonlyRIrare) =  2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  139"
[1] "V only rare iSNPs (VonlyRIrare) =  116"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  4155"
[1] "All rare fixed SNPs (AllFrare) =  780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  19"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  8"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 24 rows containing missing values (geom_point).
Warning: Removed 103 rows containing missing values (geom_point).
Warning: Removed 884 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1064"
[1] "Number cDenovo Non-Ref SNPs for C =  4410"
[1] "Number cDenovo iSNPs for C =  1"
[1] "Number cDenovo Ref SNPs for R =  1040"
[1] "Number cDenovo Non-Ref SNPs for R =  4355"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  850"
[1] "Number cDenovo Non-Ref SNPs for V =  3642"
[1] "Number cDenovo iSNPs for V =  123"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 1011 rows containing non-finite values (stat_boxplot).

Subject 1176

SNP_analysis_pipeline(subject_id = 1176)

[1] "SUBJECT_ID is 1176"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  46106"
[1] "Num bases in R recomb = blocks 21526"
[1] "Num bases in V recomb = blocks 4302"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1038149"
[1] "Numbers of C bases above cutoff is  1035843"
[1] "Numbers of V bases above cutoff is  1027021"
[1] "Number of iSNP positions =  6142"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  62"
[1] "R only rare iSNPs (RonlyRIrare) =  29"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  40"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  6"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  1"
[1] "V only fixed SNPs (VonlyF) =  1"
[1] "V only rare fixed SNPs (VonlyFrare) =  1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  528"
[1] "V only rare iSNPs (VonlyRIrare) =  303"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  45"
[1] "RC only fixed SNPs (RConlyF) =  53"
[1] "RC only rare fixed SNPs (RConlyFrare) =  25"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  330"
[1] "RC only rare iSNPs (RConlyRIrare) =  90"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  165"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  18"
[1] "RV only rare iSNPs (RVonlyRIrare) =  5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  7"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  380"
[1] "All rare fixed SNPs (AllFrare) =  372"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  36"
[1] "All iSNPs (AllRI) =  322"
[1] "All rare  iSNPs (AllRIrare) =  88"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  82"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  7"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  7"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  41"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  504"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  59"

Warning: Removed 28 rows containing missing values (geom_point).
Warning: Removed 19 rows containing missing values (geom_point).
Warning: Removed 94 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1029"
[1] "Number cDenovo Non-Ref SNPs for C =  4311"
[1] "Number cDenovo iSNPs for C =  134"
[1] "Number cDenovo Ref SNPs for R =  1020"
[1] "Number cDenovo Non-Ref SNPs for R =  3944"
[1] "Number cDenovo iSNPs for R =  519"
[1] "Number cDenovo Ref SNPs for V =  621"
[1] "Number cDenovo Non-Ref SNPs for V =  337"
[1] "Number cDenovo iSNPs for V =  4450"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 141 rows containing non-finite values (stat_boxplot).

Subject 1182

SNP_analysis_pipeline(subject_id = 1182)

[1] "SUBJECT_ID is 1182"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 9959"
[1] "Num bases in V recomb = blocks 22563"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036038"
[1] "Numbers of C bases above cutoff is  1029053"
[1] "Numbers of V bases above cutoff is  1035249"
[1] "Number of iSNP positions =  5725"
[1] "R only fixed SNPs (RonlyF) =  20"
[1] "R only rare fixed SNPs (RonlyFrare) =  13"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  361"
[1] "R only rare iSNPs (RonlyRIrare) =  165"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  36"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  10"
[1] "C only rare iSNPs (ConlyRIrare) =  7"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  5"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  2"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  19"
[1] "RV only rare iSNPs (RVonlyRIrare) =  8"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  3"
[1] "VC only fixed SNPs (VConlyF) =  470"
[1] "VC only rare fixed SNPs (VConlyFrare) =  207"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  46"
[1] "VC only iSNPs (VConlyRI) =  27"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  10"
[1] "All fixed SNPs (AllF) =  241"
[1] "All rare fixed SNPs (AllFrare) =  218"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  60"
[1] "All iSNPs (AllRI) =  3"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  91"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  31"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  508"

Warning: Removed 91 rows containing missing values (geom_point).
Warning: Removed 27 rows containing missing values (geom_point).
Warning: Removed 54 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1057"
[1] "Number cDenovo Non-Ref SNPs for C =  4363"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1212"
[1] "Number cDenovo Non-Ref SNPs for R =  185"
[1] "Number cDenovo iSNPs for R =  4087"
[1] "Number cDenovo Ref SNPs for V =  1047"
[1] "Number cDenovo Non-Ref SNPs for V =  3890"
[1] "Number cDenovo iSNPs for V =  520"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 172 rows containing non-finite values (stat_boxplot).

Subject 1201

SNP_analysis_pipeline(subject_id = 1201)

[1] "SUBJECT_ID is 1201"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  173"
[1] "Num bases in R recomb = blocks 256"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1038120"
[1] "Numbers of C bases above cutoff is  1025145"
[1] "Numbers of V bases above cutoff is  1037114"
[1] "Number of iSNP positions =  1147"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  11"
[1] "R only rare iSNPs (RonlyRIrare) =  2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  1086"
[1] "All rare fixed SNPs (AllFrare) =  729"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  11"
[1] "All iSNPs (AllRI) =  10"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  18"

Warning: Removed 101 rows containing missing values (geom_point).
Warning: Removed 25 rows containing missing values (geom_point).
Warning: Removed 30 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  4585"
[1] "Number cDenovo Non-Ref SNPs for C =  805"
[1] "Number cDenovo iSNPs for C =  6"
[1] "Number cDenovo Ref SNPs for R =  4642"
[1] "Number cDenovo Non-Ref SNPs for R =  820"
[1] "Number cDenovo iSNPs for R =  10"
[1] "Number cDenovo Ref SNPs for V =  4631"
[1] "Number cDenovo Non-Ref SNPs for V =  829"
[1] "Number cDenovo iSNPs for V =  7"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 156 rows containing non-finite values (stat_boxplot).

Subject 1226

SNP_analysis_pipeline(subject_id = 1226)

[1] "SUBJECT_ID is 1226"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  3764"
[1] "Num bases in R recomb = blocks 3764"
[1] "Num bases in V recomb = blocks 3764"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1018587"
[1] "Numbers of C bases above cutoff is  1035547"
[1] "Numbers of V bases above cutoff is  1033213"
[1] "Number of iSNP positions =  5206"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  26"
[1] "R only rare iSNPs (RonlyRIrare) =  22"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  2"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5134"
[1] "All rare fixed SNPs (AllFrare) =  1056"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  31"
[1] "All iSNPs (AllRI) =  24"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 32 rows containing missing values (geom_point).
Warning: Removed 73 rows containing missing values (geom_point).
Warning: Removed 43 rows containing missing values (geom_point).

[1] "Number cDenovo Ref SNPs for C =  1068"
[1] "Number cDenovo Non-Ref SNPs for C =  4396"
[1] "Number cDenovo iSNPs for C =  1"
[1] "Number cDenovo Ref SNPs for R =  1061"
[1] "Number cDenovo Non-Ref SNPs for R =  4359"
[1] "Number cDenovo iSNPs for R =  4"
[1] "Number cDenovo Ref SNPs for V =  1061"
[1] "Number cDenovo Non-Ref SNPs for V =  4393"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Warning: Removed 148 rows containing non-finite values (stat_boxplot).